| addFixedWidth | Generic method to add/update peak width |
| addPeaks | generic method to add peaks |
| analysis | 'analysis', slot of 'MassSpectra' class objects |
| analysisName | 'analysisName', slot of 'MassSpectra' class objects |
| baseObject | generic accessor method baseObject |
| baseObject-PrComp-method | constructor for PrComp |
| baseObject-PrinComp-method | constructor for PrinComp |
| binning | binning |
| bwApply | bwApply |
| calibPointNew | Generic method calibPointNew that modifies slot calibPoints |
| calibPoints | 'calibPoints', slot of 'MassSpectra' class objects |
| calibration | 'calibration', slot of 'MassSpectra' class objects |
| changePeakWidth | method changePeakWidth |
| check.extension | Check file extension |
| computeMNF | compute MNF |
| computeNoise | computeNoise |
| coordToPixel | coordToPixel coordToPixel translates xy coordinates from the... |
| coordToPixel-MassImage-numeric-method | coordToPixel |
| covDiffCalc | covDiffCalc calculates a x/y shift covariance matrix of a... |
| cReadRawPhi | Ulvac phi ToF-SIMS raw data import |
| ctable | ctable is a C++ implementation to make contingency tables |
| dim-MassImage-method | method dim for MassImage |
| dim-MassSpectra-method | method definition 'dim' for 'MassSpectra' dim is a primitive |
| EigenDecompose | EigenDecompose for the MNF analysis |
| extract.header.data | extract variable names and values from Ulvac-phi ToF-SIMS... |
| findClosestMatch | Find single value 'toMatch' in vector 'MatchIn' |
| findPeakWidth | generic method findPeakWidth |
| getTOFs | generic method to calculate and get TOFs |
| image | set a generic method for image |
| imageMatrix | generic method to obtain imageMatrix |
| import | import is the C++ code for importing iontof raw data |
| import.raw | Raw data import |
| instrument | 'instrument', slot of 'MassSpectra' class objects |
| iters | generic accessor for iters slot |
| iters-MCR-method | MCR accessor iters, |
| itzipName | defining generic accessor method for "itzipName" |
| itzipName-set | generic for setter itzipName |
| LapackGenEigen | LapackGenEigen |
| legend.col | legend.col |
| look.for.itzip.property | Get ITZIP property value |
| MAF | Class MAF |
| makeTIC | generic for makeTIC |
| makeTIC-MassSpectra-method | Method makeTIC for MassSpectra Class |
| manualSelectPeaks | This method is base method for plotting and manual select... |
| MassImage | Class MassImage |
| MassSpectra | Class 'MassSpectra' |
| MCR | Class MCR |
| MNF | Class MNF |
| mz | mz getter method |
| nComp | generic accessor method for slot nComp |
| ndim | generic accessor method for slot ndim |
| ndim-MassSpectra-method | method definition 'ndim' on 'MassSpectra' |
| nearestNeighbourMean | nearestNeighbourMean |
| nnMean | nnMean is C++ code for calculating nearest neighbour means in... |
| nnMNF | Class nnMNF |
| noPlottingData | generic method for 'noPlottingData' aka 'is.null' |
| noPlottingData-PCA-method | Check NULL PCA object |
| nPeaks | generic method for nPeaks |
| nz | 'nz', slot of 'MassSpectra' class objects |
| overlayPlot | generic overlayPlot |
| parIndicesSearch | helper function for parallel processing in rawdata import... |
| PCA-class | Class PCA |
| pcaLoadings | generic accessor for slot pcaLoadings |
| pcaMAF | helper function for MAF calculation |
| PCAnalysis | Class PCAnalysis |
| pcaScores | generic accessor for slot pcaScores |
| peakIDs | 'peakIDs', slot of 'PeakList' class objects |
| PeakList | Class PeakList |
| peakMzs | 'peakMzs', slot of 'PeakList' class objects |
| peakPick | generic method peak.pick |
| peaks2Spectra | generic method peaks2Spectra |
| peakWidths | Generic method peakWidths |
| plot | Generic method for plot |
| plot-MassImage-missing-method | Method 'plot()' for 'MassImage' |
| plot-PeakList-missing-method | Method 'plot()' for 'MassSpectra' |
| points | generic method points generic method points |
| poissonScaling | generic method for "poissonScaling" |
| PrComp | Class PrComp |
| PrinComp | Class PrinComp |
| readBIF | ToF-SIMS BIF/BIF6 file import |
| recalibrate | Generic method recalibrate |
| reduceSpectrumResolution | generic method reduceSpectrumResolution |
| removePeaks | generic method removePeaks |
| resids | generic accessor method for resids |
| resids-MCR-method | MCR accessor resids, |
| RSS | generic accessor for RSS |
| RSS-MCR-method | MCR accessor RSS, |
| scale | generic for scale |
| show-MassImage-method | method definition 'show' on 'MassImage' show has a generic by... |
| show-MassSpectra-method | method defining 'show()' for the 'MassSpectra' class show has... |
| show-PeakList-method | method defining 'show()' for the 'MassSpectra' class show has... |
| smootherGolay | generic method smootherGolay |
| smootherSpline | generic smootherSpline |
| smoothScatter | generic for smoothScatter |
| SNR | Signal-to-Noise Ratio (SNR) |
| subset | Generic method for subset |
| tofsims-package | ToF-SIMS Toolbox (tofsims) |
| unitMassPeaks | Generic method for unitMassPeaks |
| validMassImageObject | Validation method functionf for class MassImage objects |
| validMassSpectraObject | Validation method function for class MassImage objects |
| validPCAObject | Validation method function for class PCA objects |
| validPeakListObject | Validation method function for class PeakList objects |
| xdim | generic accessor method for "xdim" |
| xdim-MassImage-method | Getter, method definition "xdim" on "MassImage" |
| xdim-PCA-method | method xdim() for PCA class object |
| xdim-set | generic setter method for "xdim" |
| xy | 'xy', slot of 'MassImage' class objects |
| xySpec | Generic method 'xySpec' |
| ydim | generic accessor method for "ydim" |
| ydim-MassImage-method | Getter, method definition "ydim" on "MassImage" |
| ydim-PCA-method | method ydim() for PCA class object |
| ydim-set | generic setter method for "ydim" |
| zdim | generic accessor method for "zdim" |
| zdim-MassSpectra-method | method definition 'zdim' on 'MassSpectra' |
